1
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Pastic A, Nosella ML, Kochhar A, Liu ZH, Forman-Kay JD, D'Amours D. Chromosome compaction is triggered by an autonomous DNA-binding module within condensin. Cell Rep 2024; 43:114419. [PMID: 38985672 DOI: 10.1016/j.celrep.2024.114419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 04/16/2024] [Accepted: 06/14/2024] [Indexed: 07/12/2024] Open
Abstract
The compaction of chromatin into mitotic chromosomes is essential for faithful transmission of the genome during cell division. In eukaryotes, chromosome morphogenesis is regulated by the condensin complex, though the exact mechanism used to target condensin to chromatin and initiate condensation is not understood. Here, we reveal that condensin contains an intrinsically disordered region (IDR) that modulates its association with chromatin in early mitosis and exhibits phase separation. We describe DNA-binding motifs within the IDR that, upon deletion, inflict striking defects in chromosome condensation and segregation, ill-timed condensin turnover on chromatin, and cell death. Importantly, we demonstrate that the condensin IDR can impart cell cycle regulatory functions when transferred to other subunits within the complex, indicating its autonomous nature. Collectively, our study unveils the molecular basis for the initiation of chromosome condensation in early mitosis and how this process ultimately promotes genomic stability and faultless cell division.
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Affiliation(s)
- Alyssa Pastic
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Michael L Nosella
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Annahat Kochhar
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Zi Hao Liu
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Julie D Forman-Kay
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Damien D'Amours
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada.
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2
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Ziaei Jam H, Zook JM, Javadzadeh S, Park J, Sehgal A, Gymrek M. LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads. Genome Biol 2024; 25:176. [PMID: 38965568 PMCID: PMC11229021 DOI: 10.1186/s13059-024-03319-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/21/2024] [Indexed: 07/06/2024] Open
Abstract
Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve tandem repeat analysis, especially for long or complex repeats. Here, we introduce LongTR, which accurately genotypes tandem repeats from high-fidelity long reads available from both PacBio and Oxford Nanopore Technologies. LongTR is freely available at https://github.com/gymrek-lab/longtr and https://zenodo.org/doi/10.5281/zenodo.11403979 .
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Affiliation(s)
- Helyaneh Ziaei Jam
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Justin M Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, MD, USA
| | - Sara Javadzadeh
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Jonghun Park
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Aarushi Sehgal
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Melissa Gymrek
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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3
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Vegezzi E, Ishiura H, Bragg DC, Pellerin D, Magrinelli F, Currò R, Facchini S, Tucci A, Hardy J, Sharma N, Danzi MC, Zuchner S, Brais B, Reilly MM, Tsuji S, Houlden H, Cortese A. Neurological disorders caused by novel non-coding repeat expansions: clinical features and differential diagnosis. Lancet Neurol 2024; 23:725-739. [PMID: 38876750 DOI: 10.1016/s1474-4422(24)00167-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 06/16/2024]
Abstract
Nucleotide repeat expansions in the human genome are a well-known cause of neurological disease. In the past decade, advances in DNA sequencing technologies have led to a better understanding of the role of non-coding DNA, that is, the DNA that is not transcribed into proteins. These techniques have also enabled the identification of pathogenic non-coding repeat expansions that cause neurological disorders. Mounting evidence shows that adult patients with familial or sporadic presentations of epilepsy, cognitive dysfunction, myopathy, neuropathy, ataxia, or movement disorders can be carriers of non-coding repeat expansions. The description of the clinical, epidemiological, and molecular features of these recently identified non-coding repeat expansion disorders should guide clinicians in the diagnosis and management of these patients, and help in the genetic counselling for patients and their families.
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Affiliation(s)
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - D Cristopher Bragg
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David Pellerin
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, QC, Canada
| | - Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Riccardo Currò
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Stefano Facchini
- IRCCS Mondino Foundation, Pavia, Italy; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Arianna Tucci
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK
| | - John Hardy
- Department of Neurogedengerative Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Nutan Sharma
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Matt C Danzi
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Stephan Zuchner
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Bernard Brais
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, QC, Canada
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Institute of Medical Genomics, International University of Health and Welfare, Chiba, Japan
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Andrea Cortese
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK; Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy.
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4
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Kim JH, Koh IG, Lee H, Lee GH, Song DY, Kim SW, Kim Y, Han JH, Bong G, Lee J, Byun H, Son JH, Kim YR, Lee Y, Kim JJ, Park JW, Kim IB, Choi JK, Jang JH, Trost B, Lee J, Kim E, Yoo HJ, An JY. Short tandem repeat expansions in cortical layer-specific genes implicate in phenotypic severity and adaptability of autism spectrum disorder. Psychiatry Clin Neurosci 2024; 78:405-415. [PMID: 38751214 DOI: 10.1111/pcn.13676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/14/2024] [Accepted: 04/15/2024] [Indexed: 07/06/2024]
Abstract
AIM Short tandem repeats (STRs) are repetitive DNA sequences and highly mutable in various human disorders. While the involvement of STRs in various genetic disorders has been extensively studied, their role in autism spectrum disorder (ASD) remains largely unexplored. In this study, we aimed to investigate genetic association of STR expansions with ASD using whole genome sequencing (WGS) and identify risk loci associated with ASD phenotypes. METHODS We analyzed WGS data of 634 ASD families and performed genome-wide evaluation for 12,929 STR loci. We found rare STR expansions that exceeded normal repeat lengths in autism cases compared to unaffected controls. By integrating single cell RNA and ATAC sequencing datasets of human postmortem brains, we prioritized STR loci in genes specifically expressed in cortical development stages. A deep learning method was used to predict functionality of ASD-associated STR loci. RESULTS In ASD cases, rare STR expansions predominantly occurred in early cortical layer-specific genes involved in neurodevelopment, highlighting the cellular specificity of STR-associated genes in ASD risk. Leveraging deep learning prediction models, we demonstrated that these STR expansions disrupted the regulatory activity of enhancers and promoters, suggesting a potential mechanism through which they contribute to ASD pathogenesis. We found that individuals with ASD-associated STR expansions exhibited more severe ASD phenotypes and diminished adaptability compared to non-carriers. CONCLUSION Short tandem repeat expansions in cortical layer-specific genes are associated with ASD and could potentially be a risk genetic factor for ASD. Our study is the first to show evidence of STR expansion associated with ASD in an under-investigated population.
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Affiliation(s)
- Jae Hyun Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - In Gyeong Koh
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Hyeji Lee
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Gang-Hee Lee
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Da-Yea Song
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soo-Whee Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Yujin Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Jae Hyun Han
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, College of Medicine, Soonchunhyang University Cheonan Hospital, Cheonan, Republic of Korea
| | - Guiyoung Bong
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeewon Lee
- Department of Psychiatry, Soonchunhyang University College of Medicine, Asan, Republic of Korea
| | - Heejung Byun
- Department of Neuropsychiatry, Seoul Metropolitan Children's Hospital, Seoul, Republic of Korea
| | - Ji Hyun Son
- Department of Neuropsychiatry, Seoul Metropolitan Children's Hospital, Seoul, Republic of Korea
| | - Ye Rim Kim
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoojeong Lee
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Justine Jaewon Kim
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jung Woo Park
- Center for Biomedical Computing, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, Republic of Korea
| | - Il Bin Kim
- Department of Psychiatry, Hanyang University Guri Hospital, Guri, Republic of Korea
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Brett Trost
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Junehawk Lee
- Center for Biomedical Computing, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, Republic of Korea
| | - Eunjoon Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Hee Jeong Yoo
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Psychiatry, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul, Republic of Korea
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, Republic of Korea
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5
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Rajan-Babu IS, Dolzhenko E, Eberle MA, Friedman JM. Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications. Nat Rev Genet 2024; 25:476-499. [PMID: 38467784 DOI: 10.1038/s41576-024-00696-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/13/2024]
Abstract
Short tandem repeats (STRs) are a class of repetitive elements, composed of tandem arrays of 1-6 base pair sequence motifs, that comprise a substantial fraction of the human genome. STR expansions can cause a wide range of neurological and neuromuscular conditions, known as repeat expansion disorders, whose age of onset, severity, penetrance and/or clinical phenotype are influenced by the length of the repeats and their sequence composition. The presence of non-canonical motifs, depending on the type, frequency and position within the repeat tract, can alter clinical outcomes by modifying somatic and intergenerational repeat stability, gene expression and mutant transcript-mediated and/or protein-mediated toxicities. Here, we review the diverse structural conformations of repeat expansions, technological advances for the characterization of changes in sequence composition, their clinical correlations and the impact on disease mechanisms.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada.
| | | | | | - Jan M Friedman
- Department of Medical Genetics, The University of British Columbia, and Children's & Women's Hospital, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
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6
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Gao J, Li F. Heterochromatin repeat organization at an individual level: Rex1BD and the 14-3-3 protein coordinate to shape the epigenetic landscape within heterochromatin repeats. Bioessays 2024; 46:e2400030. [PMID: 38679759 DOI: 10.1002/bies.202400030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024]
Abstract
In eukaryotic cells, heterochromatin is typically composed of tandem DNA repeats and plays crucial roles in gene expression and genome stability. It has been reported that silencing at individual units within tandem heterochromatin repeats exhibits a position-dependent variation. However, how the heterochromatin is organized at an individual repeat level remains poorly understood. Using a novel genetic approach, our recent study identified a conserved protein Rex1BD required for position-dependent silencing within heterochromatin repeats. We further revealed that Rex1BD interacts with the 14-3-3 protein to regulate heterochromatin silencing by linking RNAi and HDAC pathways. In this review, we discuss how Rex1BD and the 14-3-3 protein coordinate to modulate heterochromatin organization at the individual repeat level, and comment on the biological significance of the position-dependent effect in heterochromatin repeats. We also identify the knowledge gaps that still need to be unveiled in the field.
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Affiliation(s)
- Jinxin Gao
- Department of Biology, New York University, New York, New York, USA
| | - Fei Li
- Department of Biology, New York University, New York, New York, USA
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7
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Alizadeh S, Khamse S, Vafadar S, Bernhart SH, Afshar H, Vahedi M, Rezaei O, Delbari A, Ohadi M. The human SMAD9 (GCC) repeat links to natural selection and late-onset neurocognitive disorders. Neurol Sci 2024:10.1007/s10072-024-07637-y. [PMID: 38877206 DOI: 10.1007/s10072-024-07637-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
INTRODUCTION Whereas (GCC)-repeats are overrepresented in genic regions, and mutation hotspots, they are largely unexplored with regard to their link with natural selection. Across numerous primate species and tissues, SMAD9 (SMAD Family Member 9) reaches highest level of expression in the human brain. This gene contains a (GCC)-repeat in the interval between + 1 and + 60 of the transcription start site, which is in the high-ranking (GCC)-repeats with respect to length. METHODS Here we sequenced this (GCC)-repeat in 396 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 181) and controls (N = 215). RESULTS We detected two predominantly abundant alleles of 7 and 9 repeats, forming 96.2% of the allele pool. The (GCC)7/(GCC)9 ratio was in the reverse order in the NCD group versus controls (p = 0.005), resulting from excess of (GCC)7 in the NCD group (p = 0.003) and (GCC)9 in the controls (p = 0.01). Five genotypes, predominantly consisting of (GCC)7 and lacking (GCC)9 were detected in the NCD group only (p = 0.008). The patients harboring those genotypes received the diagnoses of Alzheimer's disease (AD) and vascular dementia (VD). Five genotypes consisting of (GCC)9 and lacking (GCC)7 were detected in the control group only (p = 0.002). The group-specific genotypes formed approximately 4% of the genotype pool in the human samples studied. CONCLUSION We propose natural selection and a novel locus for late-onset AD and VD at the SMAD9 (GCC)-repeat in humans.
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Affiliation(s)
- Samira Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran
| | - Safoura Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran
| | - Sara Vafadar
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran
| | - Stephan H Bernhart
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107, Leipzig, Germany
| | - Hossein Afshar
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran
| | - Mohsen Vahedi
- Department of Biostatistics and Epidemiology, Paediatric Neurorehabilitation Research Centre, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Omid Rezaei
- Department of Psychiatry, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Ahmad Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran.
| | - Mina Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Daneshjoo Blvd. Koodakyar St, Tehran, 1985713871, Iran.
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8
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Parmar JM, Laing NG, Kennerson ML, Ravenscroft G. Genetics of inherited peripheral neuropathies and the next frontier: looking backwards to progress forwards. J Neurol Neurosurg Psychiatry 2024:jnnp-2024-333436. [PMID: 38744462 DOI: 10.1136/jnnp-2024-333436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Inherited peripheral neuropathies (IPNs) encompass a clinically and genetically heterogeneous group of disorders causing length-dependent degeneration of peripheral autonomic, motor and/or sensory nerves. Despite gold-standard diagnostic testing for pathogenic variants in over 100 known associated genes, many patients with IPN remain genetically unsolved. Providing patients with a diagnosis is critical for reducing their 'diagnostic odyssey', improving clinical care, and for informed genetic counselling. The last decade of massively parallel sequencing technologies has seen a rapid increase in the number of newly described IPN-associated gene variants contributing to IPN pathogenesis. However, the scarcity of additional families and functional data supporting variants in potential novel genes is prolonging patient diagnostic uncertainty and contributing to the missing heritability of IPNs. We review the last decade of IPN disease gene discovery to highlight novel genes, structural variation and short tandem repeat expansions contributing to IPN pathogenesis. From the lessons learnt, we provide our vision for IPN research as we anticipate the future, providing examples of emerging technologies, resources and tools that we propose that will expedite the genetic diagnosis of unsolved IPN families.
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Affiliation(s)
- Jevin M Parmar
- Rare Disease Genetics and Functional Genomics, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Nigel G Laing
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Preventive Genetics, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, New South Wales, Australia
| | - Gianina Ravenscroft
- Rare Disease Genetics and Functional Genomics, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
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9
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Hiatt L, Weisburd B, Dolzhenko E, VanNoy GE, Kurtas EN, Rehm HL, Quinlan A, Dashnow H. STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.21.24307682. [PMID: 38826469 PMCID: PMC11142282 DOI: 10.1101/2024.05.21.24307682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Approximately 3% of the human genome consists of repetitive elements called tandem repeats (TRs), which include short tandem repeats (STRs) of 1-6bp motifs and variable number tandem repeats (VNTRs) of 7+bp motifs. TR variants contribute to several dozen mono- and polygenic diseases but remain understudied and "enigmatic," particularly relative to single nucleotide variants. It remains comparatively challenging to interpret the clinical significance of TR variants. Although existing resources provide portions of necessary data for interpretation at disease-associated loci, it is currently difficult or impossible to efficiently invoke the additional details critical to proper interpretation, such as motif pathogenicity, disease penetrance, and age of onset distributions. It is also often unclear how to apply population information to analyses. We present STRchive (S-T-archive, http://strchive.org/ ), a dynamic resource consolidating information on TR disease loci in humans from research literature, up-to-date clinical resources, and large-scale genomic databases, with the goal of streamlining TR variant interpretation at disease-associated loci. We apply STRchive -including pathogenic thresholds, motif classification, and clinical phenotypes-to a gnomAD cohort of ∼18.5k individuals genotyped at 60 disease-associated loci. Through detailed literature curation, we demonstrate that the majority of TR diseases affect children despite being thought of as adult diseases. Additionally, we show that pathogenic genotypes can be found within gnomAD which do not necessarily overlap with known disease prevalence, and leverage STRchive to interpret locus-specific findings therein. We apply a diagnostic blueprint empowered by STRchive to relevant clinical vignettes, highlighting possible pitfalls in TR variant interpretation. As a living resource, STRchive is maintained by experts, takes community contributions, and will evolve as understanding of TR diseases progresses.
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10
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Currò R, Dominik N, Facchini S, Vegezzi E, Sullivan R, Galassi Deforie V, Fernández-Eulate G, Traschütz A, Rossi S, Garibaldi M, Kwarciany M, Taroni F, Brusco A, Good JM, Cavalcanti F, Hammans S, Ravenscroft G, Roxburgh RH, Parolin Schnekenberg R, Rugginini B, Abati E, Manini A, Quartesan I, Ghia A, Lòpez de Munaìn A, Manganelli F, Kennerson M, Santorelli FM, Infante J, Marques W, Jokela M, Murphy SM, Mandich P, Fabrizi GM, Briani C, Gosal D, Pareyson D, Ferrari A, Prados F, Yousry T, Khurana V, Kuo SH, Miller J, Troakes C, Jaunmuktane Z, Giunti P, Hartmann A, Basak N, Synofzik M, Stojkovic T, Hadjivassiliou M, Reilly MM, Houlden H, Cortese A. Role of the repeat expansion size in predicting age of onset and severity in RFC1 disease. Brain 2024; 147:1887-1898. [PMID: 38193360 PMCID: PMC11068103 DOI: 10.1093/brain/awad436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 01/10/2024] Open
Abstract
RFC1 disease, caused by biallelic repeat expansion in RFC1, is clinically heterogeneous in terms of age of onset, disease progression and phenotype. We investigated the role of the repeat size in influencing clinical variables in RFC1 disease. We also assessed the presence and role of meiotic and somatic instability of the repeat. In this study, we identified 553 patients carrying biallelic RFC1 expansions and measured the repeat expansion size in 392 cases. Pearson's coefficient was calculated to assess the correlation between the repeat size and age at disease onset. A Cox model with robust cluster standard errors was adopted to describe the effect of repeat size on age at disease onset, on age at onset of each individual symptoms, and on disease progression. A quasi-Poisson regression model was used to analyse the relationship between phenotype and repeat size. We performed multivariate linear regression to assess the association of the repeat size with the degree of cerebellar atrophy. Meiotic stability was assessed by Southern blotting on first-degree relatives of 27 probands. Finally, somatic instability was investigated by optical genome mapping on cerebellar and frontal cortex and unaffected peripheral tissue from four post-mortem cases. A larger repeat size of both smaller and larger allele was associated with an earlier age at neurological onset [smaller allele hazard ratio (HR) = 2.06, P < 0.001; larger allele HR = 1.53, P < 0.001] and with a higher hazard of developing disabling symptoms, such as dysarthria or dysphagia (smaller allele HR = 3.40, P < 0.001; larger allele HR = 1.71, P = 0.002) or loss of independent walking (smaller allele HR = 2.78, P < 0.001; larger allele HR = 1.60; P < 0.001) earlier in disease course. Patients with more complex phenotypes carried larger expansions [smaller allele: complex neuropathy rate ratio (RR) = 1.30, P = 0.003; cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) RR = 1.34, P < 0.001; larger allele: complex neuropathy RR = 1.33, P = 0.008; CANVAS RR = 1.31, P = 0.009]. Furthermore, larger repeat expansions in the smaller allele were associated with more pronounced cerebellar vermis atrophy (lobules I-V β = -1.06, P < 0.001; lobules VI-VII β = -0.34, P = 0.005). The repeat did not show significant instability during vertical transmission and across different tissues and brain regions. RFC1 repeat size, particularly of the smaller allele, is one of the determinants of variability in RFC1 disease and represents a key prognostic factor to predict disease onset, phenotype and severity. Assessing the repeat size is warranted as part of the diagnostic test for RFC1 expansion.
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Affiliation(s)
- Riccardo Currò
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Natalia Dominik
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Stefano Facchini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | | | - Roisin Sullivan
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | | | - Gorka Fernández-Eulate
- Nord/Est/Ile-de-France Neuromuscular Reference Center, Institute of Myology, Pitié-Salpêtrière Hospital, APHP, 75013 Paris, France
| | - Andreas Traschütz
- Research Division ‘Translational Genomics of Neurodegenerative Diseases’, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, 72076 Tübingen, Germany
| | - Salvatore Rossi
- Dipartimento di Scienze dell'Invecchiamento, Neurologiche, Ortopediche e della Testa-Collo, UOC Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Facoltà di Medicina e Chirurgia, Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Matteo Garibaldi
- Neuromuscular and Rare Disease Center, Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Sant'Andrea Hospital, Sapienza University of Rome, 00189 Rome, Italy
| | - Mariusz Kwarciany
- Department of Adult Neurology, Medical University of Gdańsk, 80-952 Gdańsk, Poland
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10124 Turin, Italy
| | - Jean-Marc Good
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Francesca Cavalcanti
- Institute for Biomedical Research and Innovation (IRIB), Italian National Research Council (CNR), 87050 Mangone, Italy
| | - Simon Hammans
- Wessex Neurological Centre, Southampton General Hospital, Southampton, SO16 6YD, UK
| | - Gianina Ravenscroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedland, WA 6009, Australia
| | - Richard H Roxburgh
- Neurology Department, Auckland City Hospital, New Zealand and the Centre for Brain Research, University of Auckland, Auckland 1142, New Zealand
| | | | - Bianca Rugginini
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Elena Abati
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Arianna Manini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Ilaria Quartesan
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Arianna Ghia
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Adolfo Lòpez de Munaìn
- Neurology Department, Donostia University Hospital, University of the Basque Country-Osakidetza-CIBERNED-Biodonostia, 20014 Donostia-San Sebastián, Spain
| | - Fiore Manganelli
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, University of Naples Federico II, 80131 Naples, Italy
| | - Marina Kennerson
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2050, Australia
| | - Filippo Maria Santorelli
- IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Disease Unit, 56128 Pisa, Italy
| | - Jon Infante
- University Hospital Marquès de Valdecilla-IDIVAL, University of Cantabria, 39008 Santander, Spain
| | - Wilson Marques
- Department of Neurology, School of Medicine of Ribeirão Preto, University of São Paulo, 2650 Ribeirão Preto, Brazil
| | - Manu Jokela
- Neuromuscular Research Center, Department of Neurology, Tampere University and University Hospital, 33520 Tampere, Finland
- Neurocenter, Department of Neurology, Clinical Neurosciences, Turku University Hospital and University of Turku, 20014 Turku, Finland
| | - Sinéad M Murphy
- Department of Neurology, Tallaght University Hospital, D24 NR0A Dublin, Ireland
- Academic Unit of Neurology, Trinity College Dublin, D02 R590 Dublin, Ireland
| | - Paola Mandich
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy
- IRCCS Ospedale Policlinico San Martino-UOC Genetica Medica, 16132 Genova, Italy
| | - Gian Maria Fabrizi
- Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, 37134 Verona, Italy
| | - Chiara Briani
- Department of Neurosciences, ERN Neuromuscular Unit, University of Padova, 35100 Padova, Italy
| | - David Gosal
- Manchester Centre for Clinical Neurosciences, Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Greater Manchester, M6 8HD, UK
| | - Davide Pareyson
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
| | | | - Ferran Prados
- Centre for Medical Image Computing (CMIC), Department of Medical Physics and Biomedical Engineering, University College London, London, WC1V 6LJ, UK
- NMR Research Unit, Institute of Neurology, University College London (UCL), London, WC1N 3BG, UK
- e-Health Centre, Universitat Oberta de Catalunya, 08018 Barcelona, Spain
| | - Tarek Yousry
- Neuroradiological Academic Unit, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Vikram Khurana
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sheng-Han Kuo
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - James Miller
- Department of Neurology, Royal Victoria Hospitals, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, NE1 4LP, UK
| | - Claire Troakes
- London Neurodegenerative Diseases Brain Bank, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE21 8EA, UK
| | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Paola Giunti
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Annette Hartmann
- Division of General Psychiatry, Medical University of Vienna, 1090 Vienna, Austria
| | - Nazli Basak
- Koç University, School of Medicine, Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Research Center for Translational Medicine, 34010 Istanbul, Turkey
| | - Matthis Synofzik
- Research Division ‘Translational Genomics of Neurodegenerative Diseases’, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, 72076 Tübingen, Germany
| | - Tanya Stojkovic
- Nord/Est/Ile-de-France Neuromuscular Reference Center, Institute of Myology, Pitié-Salpêtrière Hospital, APHP, 75013 Paris, France
| | - Marios Hadjivassiliou
- Academic Department of Neurosciences, Sheffield Teaching Hospitals NHS Trust and University of Sheffield, Sheffield, S10 2JF, UK
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Andrea Cortese
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
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11
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Pires GP, Fioresi VS, Canal D, Canal DC, Fernandes M, Brustolini OJB, de Avelar Carpinetti P, Ferreira A, da Silva Ferreira MF. Effects of trimer repeats on Psidium guajava L. gene expression and prospection of functional microsatellite markers. Sci Rep 2024; 14:9811. [PMID: 38684872 PMCID: PMC11059378 DOI: 10.1038/s41598-024-60417-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/23/2024] [Indexed: 05/02/2024] Open
Abstract
Most research on trinucleotide repeats (TRs) focuses on human diseases, with few on the impact of TR expansions on plant gene expression. This work investigates TRs' effect on global gene expression in Psidium guajava L., a plant species with widespread distribution and significant relevance in the food, pharmacology, and economics sectors. We analyzed TR-containing coding sequences in 1,107 transcripts from 2,256 genes across root, shoot, young leaf, old leaf, and flower bud tissues of the Brazilian guava cultivars Cortibel RM and Paluma. Structural analysis revealed TR sequences with small repeat numbers (5-9) starting with cytosine or guanine or containing these bases. Functional annotation indicated TR-containing genes' involvement in cellular structures and processes (especially cell membranes and signal recognition), stress response, and resistance. Gene expression analysis showed significant variation, with a subset of highly expressed genes in both cultivars. Differential expression highlighted numerous down-regulated genes in Cortibel RM tissues, but not in Paluma, suggesting interplay between tissues and cultivars. Among 72 differentially expressed genes with TRs, 24 form miRNAs, 13 encode transcription factors, and 11 are associated with transposable elements. In addition, a set of 20 SSR-annotated, transcribed, and differentially expressed genes with TRs was selected as phenotypic markers for Psidium guajava and, potentially for closely related species as well.
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Affiliation(s)
- Giovanna Pinto Pires
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Vinicius Sartori Fioresi
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Drielli Canal
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Dener Cezati Canal
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Miquéias Fernandes
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Otávio José Bernardes Brustolini
- Laboratório Nacional de Computação Científica (LNCC). Av. Getulio Vargas, 333, Petrópolis, Rio de Janeiro, Quitandinha, 25651-076, Brazil
| | - Paola de Avelar Carpinetti
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Adésio Ferreira
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil
| | - Marcia Flores da Silva Ferreira
- Centro de Ciências Agrárias e Engenharias, Departamento de Agronomia, Universidade Federal Do Espírito Santo, Alto Universitário, s/n, Alegre, ES, 29500-000, Brazil.
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12
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English AC, Dolzhenko E, Ziaei Jam H, McKenzie SK, Olson ND, De Coster W, Park J, Gu B, Wagner J, Eberle MA, Gymrek M, Chaisson MJP, Zook JM, Sedlazeck FJ. Analysis and benchmarking of small and large genomic variants across tandem repeats. Nat Biotechnol 2024:10.1038/s41587-024-02225-z. [PMID: 38671154 DOI: 10.1038/s41587-024-02225-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/28/2024] [Indexed: 04/28/2024]
Abstract
Tandem repeats (TRs) are highly polymorphic in the human genome, have thousands of associated molecular traits and are linked to over 60 disease phenotypes. However, they are often excluded from at-scale studies because of challenges with variant calling and representation, as well as a lack of a genome-wide standard. Here, to promote the development of TR methods, we created a catalog of TR regions and explored TR properties across 86 haplotype-resolved long-read human assemblies. We curated variants from the Genome in a Bottle (GIAB) HG002 individual to create a TR dataset to benchmark existing and future TR analysis methods. We also present an improved variant comparison method that handles variants greater than 4 bp in length and varying allelic representation. The 8.1% of the genome covered by the TR catalog holds ~24.9% of variants per individual, including 124,728 small and 17,988 large variants for the GIAB HG002 'truth-set' TR benchmark. We demonstrate the utility of this pipeline across short-read and long-read technologies.
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Affiliation(s)
- Adam C English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | | | - Helyaneh Ziaei Jam
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | | | - Nathan D Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Jonghun Park
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Bida Gu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Melissa Gymrek
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Justin M Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
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13
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Cui Y, Ye W, Li JS, Li JJ, Vilain E, Sallam T, Li W. A genome-wide spectrum of tandem repeat expansions in 338,963 humans. Cell 2024; 187:2336-2341.e5. [PMID: 38582080 PMCID: PMC11065452 DOI: 10.1016/j.cell.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/23/2024] [Accepted: 03/05/2024] [Indexed: 04/08/2024]
Abstract
The Genome Aggregation Database (gnomAD), widely recognized as the gold-standard reference map of human genetic variation, has largely overlooked tandem repeat (TR) expansions, despite the fact that TRs constitute ∼6% of our genome and are linked to over 50 human diseases. Here, we introduce the TR-gnomAD (https://wlcb.oit.uci.edu/TRgnomAD), a biobank-scale reference of 0.86 million TRs derived from 338,963 whole-genome sequencing (WGS) samples of diverse ancestries (39.5% non-European samples). TR-gnomAD offers critical insights into ancestry-specific disease prevalence using disparities in TR unit number frequencies among ancestries. Moreover, TR-gnomAD is able to differentiate between common, presumably benign TR expansions, which are prevalent in TR-gnomAD, from those potentially pathogenic TR expansions, which are found more frequently in disease groups than within TR-gnomAD. Together, TR-gnomAD is an invaluable resource for researchers and physicians to interpret TR expansions in individuals with genetic diseases.
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Affiliation(s)
- Ya Cui
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA.
| | - Wenbin Ye
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Jason Sheng Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric Vilain
- Institute for Clinical and Translational Science, University of California, Irvine, Irvine, CA 92697, USA; Department of Pediatrics, University of California, Irvine, Irvine, CA 92697, USA
| | - Tamer Sallam
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA.
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14
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Tajeddin N, Arabfard M, Alizadeh S, Salesi M, Khamse S, Delbari A, Ohadi M. Novel islands of GGC and GCC repeats coincide with human evolution. Gene 2024; 902:148194. [PMID: 38262548 DOI: 10.1016/j.gene.2024.148194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/29/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND Because of high mutation rate, overrepresentation in genic regions, and link with various neurological, neurodegenerative, and movement disorders, GGC and GCC short tandem repeats (STRs) are prone to natural selection. Among a number of lacking data, the 3-repeats of these STRs remain widely unexplored. RESULTS In a genome-wide search in human, here we mapped GGC and GCC STRs of ≥3-repeats, and found novel islands of up to 45 of those STRs, populating spans of 1 to 2 kb of genomic DNA. RGPD4 and NOC4L harbored the densest (GGC)3 (probability 3.09061E-71) and (GCC)3 (probability 1.72376E-61) islands, respectively, and were human-specific. We also found prime instances of directional incremented density of STRs at specific loci in human versus other species, including the FOXK2 and SKI GGC islands. The genes containing those islands significantly diverged in expression in human versus other species, and the proteins encoded by those genes interact closely in a physical interaction network, consequence of which may be human-specific characteristics such as higher order brain functions. CONCLUSION We report novel islands of GGC and GCC STRs of evolutionary relevance to human. The density, and in some instances, periodicity of these islands support them as a novel genomic entity, which need to be further explored in evolutionary, mechanistic, and functional platforms.
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Affiliation(s)
- N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Salesi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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15
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Niso-Santano M, Fuentes JM, Galluzzi L. Immunological aspects of central neurodegeneration. Cell Discov 2024; 10:41. [PMID: 38594240 PMCID: PMC11004155 DOI: 10.1038/s41421-024-00666-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/02/2024] [Indexed: 04/11/2024] Open
Abstract
The etiology of various neurodegenerative disorders that mainly affect the central nervous system including (but not limited to) Alzheimer's disease, Parkinson's disease and Huntington's disease has classically been attributed to neuronal defects that culminate with the loss of specific neuronal populations. However, accumulating evidence suggests that numerous immune effector cells and the products thereof (including cytokines and other soluble mediators) have a major impact on the pathogenesis and/or severity of these and other neurodegenerative syndromes. These observations not only add to our understanding of neurodegenerative conditions but also imply that (at least in some cases) therapeutic strategies targeting immune cells or their products may mediate clinically relevant neuroprotective effects. Here, we critically discuss immunological mechanisms of central neurodegeneration and propose potential strategies to correct neurodegeneration-associated immunological dysfunction with therapeutic purposes.
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Affiliation(s)
- Mireia Niso-Santano
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, Cáceres, Spain.
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas-Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), Madrid, Spain.
- Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), Cáceres, Spain.
| | - José M Fuentes
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, Cáceres, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas-Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), Madrid, Spain
- Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), Cáceres, Spain
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, New York, NY, USA.
- Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA.
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16
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Khamse S, Alizadeh S, Khorshid HRK, Delbari A, Tajeddin N, Ohadi M. A Hypermutable Region in the DISP2 Gene Links to Natural Selection and Late-Onset Neurocognitive Disorders in Humans. Mol Neurobiol 2024:10.1007/s12035-024-04155-y. [PMID: 38565786 DOI: 10.1007/s12035-024-04155-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 03/25/2024] [Indexed: 04/04/2024]
Abstract
(CCG) short tandem repeats (STRs) are predominantly enriched in genic regions, mutation hotspots for C to T truncating substitutions, and involved in various neurological and neurodevelopmental disorders. However, intact blocks of this class of STRs are widely overlooked with respect to their link with natural selection. The human neuron-specific gene, DISP2 (dispatched RND transporter family member 2), contains a (CCG) repeat in its 5' untranslated region. Here, we sequenced this STR in a sample of 448 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 203) and controls (N = 245). We found that the region spanning the (CCG) repeat was highly mutated, resulting in several flanking (CCG) residues. However, an 8-repeat of the (CCG) repeat was predominantly abundant (frequency = 0.92) across the two groups. While the overall distribution of genotypes was not different between the two groups (p > 0.05), we detected four genotypes in the NCD group only (2% of the NCD genotypes, Mid-p = 0.02), consisting of extreme short alleles, 5- and 6-repeats, that were not detected in the control group. The patients harboring those genotypes received the diagnoses of probable Alzheimer's disease and vascular dementia. We also found six genotypes in the control group only (2.5% of the control genotypes, Mid-p = 0.01) that consisted of the 8-repeat and extreme long alleles, 9- and 10-repeats, of which the 10-repeat was not detected in the NCD group. The (CCG) repeat specifically expanded in primates. In conclusion, we report an indication of natural selection at a novel hypermutable region in the human genome and divergent alleles and genotypes in late-onset NhCDs and controls. These findings reinforce the hypothesis that a collection of rare alleles and genotypes in a number of genes may unambiguously contribute to the cognition impairment component of late-onset NCDs.
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Affiliation(s)
- S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H R Khorram Khorshid
- Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
| | - N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Department of Biology, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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17
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Oketch JW, Wain LV, Hollox EJ. A comparison of software for analysis of rare and common short tandem repeat (STR) variation using human genome sequences from clinical and population-based samples. PLoS One 2024; 19:e0300545. [PMID: 38558075 PMCID: PMC10984476 DOI: 10.1371/journal.pone.0300545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
Short tandem repeat (STR) variation is an often overlooked source of variation between genomes. STRs comprise about 3% of the human genome and are highly polymorphic. Some cause Mendelian disease, and others affect gene expression. Their contribution to common disease is not well-understood, but recent software tools designed to genotype STRs using short read sequencing data will help address this. Here, we compare software that genotypes common STRs and rarer STR expansions genome-wide, with the aim of applying them to population-scale genomes. By using the Genome-In-A-Bottle (GIAB) consortium and 1000 Genomes Project short-read sequencing data, we compare performance in terms of sequence length, depth, computing resources needed, genotyping accuracy and number of STRs genotyped. To ensure broad applicability of our findings, we also measure genotyping performance against a set of genomes from clinical samples with known STR expansions, and a set of STRs commonly used for forensic identification. We find that HipSTR, ExpansionHunter and GangSTR perform well in genotyping common STRs, including the CODIS 13 core STRs used for forensic analysis. GangSTR and ExpansionHunter outperform HipSTR for genotyping call rate and memory usage. ExpansionHunter denovo (EHdn), STRling and GangSTR outperformed STRetch for detecting expanded STRs, and EHdn and STRling used considerably less processor time compared to GangSTR. Analysis on shared genomic sequence data provided by the GIAB consortium allows future performance comparisons of new software approaches on a common set of data, facilitating comparisons and allowing researchers to choose the best software that fulfils their needs.
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Affiliation(s)
- John W. Oketch
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Louise V. Wain
- Department of Population Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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18
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Lee M, Ahmad SF, Xu J. Regulation and function of transposable elements in cancer genomes. Cell Mol Life Sci 2024; 81:157. [PMID: 38556602 PMCID: PMC10982106 DOI: 10.1007/s00018-024-05195-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 04/02/2024]
Abstract
Over half of human genomic DNA is composed of repetitive sequences generated throughout evolution by prolific mobile genetic parasites called transposable elements (TEs). Long disregarded as "junk" or "selfish" DNA, TEs are increasingly recognized as formative elements in genome evolution, wired intimately into the structure and function of the human genome. Advances in sequencing technologies and computational methods have ushered in an era of unprecedented insight into how TE activity impacts human biology in health and disease. Here we discuss the current views on how TEs have shaped the regulatory landscape of the human genome, how TE activity is implicated in human cancers, and how recent findings motivate novel strategies to leverage TE activity for improved cancer therapy. Given the crucial role of methodological advances in TE biology, we pair our conceptual discussions with an in-depth review of the inherent technical challenges in studying repeats, specifically related to structural variation, expression analyses, and chromatin regulation. Lastly, we provide a catalog of existing and emerging assays and bioinformatic software that altogether are enabling the most sophisticated and comprehensive investigations yet into the regulation and function of interspersed repeats in cancer genomes.
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Affiliation(s)
- Michael Lee
- Department of Pediatrics, Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA.
| | - Syed Farhan Ahmad
- Department of Pathology, Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place - MS 345, Memphis, TN, 38105, USA
| | - Jian Xu
- Department of Pathology, Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place - MS 345, Memphis, TN, 38105, USA.
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19
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Duvick L, Southern WM, Benzow KA, Burch ZN, Handler HP, Mitchell JS, Kuivinen H, Gadiparthi U, Yang P, Soles A, Sheeler CA, Rainwater O, Serres S, Lind EB, Nichols-Meade T, You Y, O’Callaghan B, Zoghbi HY, Cvetanovic M, Wheeler VC, Ervasti JM, Koob MD, Orr HT. Mapping SCA1 regional vulnerabilities reveals neural and skeletal muscle contributions to disease. JCI Insight 2024; 9:e176057. [PMID: 38512434 PMCID: PMC11141930 DOI: 10.1172/jci.insight.176057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 03/19/2024] [Indexed: 03/23/2024] Open
Abstract
Spinocerebellar ataxia type 1 (SCA1) is a fatal neurodegenerative disease caused by an expanded polyglutamine tract in the widely expressed ataxin-1 (ATXN1) protein. To elucidate anatomical regions and cell types that underlie mutant ATXN1-induced disease phenotypes, we developed a floxed conditional knockin mouse (f-ATXN1146Q/2Q) with mouse Atxn1 coding exons replaced by human ATXN1 exons encoding 146 glutamines. f-ATXN1146Q/2Q mice manifested SCA1-like phenotypes including motor and cognitive deficits, wasting, and decreased survival. Central nervous system (CNS) contributions to disease were revealed using f-ATXN1146Q/2Q;Nestin-Cre mice, which showed improved rotarod, open field, and Barnes maze performance by 6-12 weeks of age. In contrast, striatal contributions to motor deficits using f-ATXN1146Q/2Q;Rgs9-Cre mice revealed that mice lacking ATXN1146Q/2Q in striatal medium-spiny neurons showed a trending improvement in rotarod performance at 30 weeks of age. Surprisingly, a prominent role for muscle contributions to disease was revealed in f-ATXN1146Q/2Q;ACTA1-Cre mice based on their recovery from kyphosis and absence of muscle pathology. Collectively, data from the targeted conditional deletion of the expanded allele demonstrated CNS and peripheral contributions to disease and highlighted the need to consider muscle in addition to the brain for optimal SCA1 therapeutics.
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Affiliation(s)
- Lisa Duvick
- Institute of Translational Neuroscience
- Department of Laboratory Medicine and Pathology, and
| | - W. Michael Southern
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kellie A. Benzow
- Institute of Translational Neuroscience
- Department of Laboratory Medicine and Pathology, and
| | - Zoe N. Burch
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Hillary P. Handler
- Institute of Translational Neuroscience
- Department of Laboratory Medicine and Pathology, and
| | - Jason S. Mitchell
- Institute of Translational Neuroscience
- Department of Laboratory Medicine and Pathology, and
| | - Hannah Kuivinen
- Institute of Translational Neuroscience
- Department of Laboratory Medicine and Pathology, and
| | - Udaya Gadiparthi
- Institute of Translational Neuroscience
- Department of Laboratory Medicine and Pathology, and
| | - Praseuth Yang
- Institute of Translational Neuroscience
- Department of Laboratory Medicine and Pathology, and
| | - Alyssa Soles
- Institute of Translational Neuroscience
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota, USA
| | - Carrie A. Sheeler
- Institute of Translational Neuroscience
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota, USA
| | - Orion Rainwater
- Institute of Translational Neuroscience
- Department of Laboratory Medicine and Pathology, and
| | - Shannah Serres
- Institute of Translational Neuroscience
- Department of Laboratory Medicine and Pathology, and
| | - Erin B. Lind
- Institute of Translational Neuroscience
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota, USA
| | - Tessa Nichols-Meade
- Institute of Translational Neuroscience
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota, USA
| | - Yun You
- Mouse Genetics Laboratory, University of Minnesota, Minneapolis. Minnesota, USA
| | - Brennon O’Callaghan
- Institute of Translational Neuroscience
- Department of Laboratory Medicine and Pathology, and
| | - Huda Y. Zoghbi
- Departments of Molecular and Human Genetics, Pediatrics, and Howard Hughes Medical Institute, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, Texas, USA
| | - Marija Cvetanovic
- Institute of Translational Neuroscience
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota, USA
| | - Vanessa C. Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA
| | - James M. Ervasti
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael D. Koob
- Institute of Translational Neuroscience
- Department of Laboratory Medicine and Pathology, and
| | - Harry T. Orr
- Institute of Translational Neuroscience
- Department of Laboratory Medicine and Pathology, and
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20
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Wang Y, Wang J, Yan Z, Hou J, Wan L, Yang Y, Liu Y, Yi J, Guo P, Han D. Structural investigation of pathogenic RFC1 AAGGG pentanucleotide repeats reveals a role of G-quadruplex in dysregulated gene expression in CANVAS. Nucleic Acids Res 2024; 52:2698-2710. [PMID: 38266156 PMCID: PMC10954463 DOI: 10.1093/nar/gkae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/26/2024] Open
Abstract
An expansion of AAGGG pentanucleotide repeats in the replication factor C subunit 1 (RFC1) gene is the genetic cause of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS), and it also links to several other neurodegenerative diseases including the Parkinson's disease. However, the pathogenic mechanism of RFC1 AAGGG repeat expansion remains enigmatic. Here, we report that the pathogenic RFC1 AAGGG repeats form DNA and RNA parallel G-quadruplex (G4) structures that play a role in impairing biological processes. We determine the first high-resolution nuclear magnetic resonance (NMR) structure of a bimolecular parallel G4 formed by d(AAGGG)2AA and reveal how AAGGG repeats fold into a higher-order structure composed of three G-tetrad layers, and further demonstrate the formation of intramolecular G4s in longer DNA and RNA repeats. The pathogenic AAGGG repeats, but not the nonpathogenic AAAAG repeats, form G4 structures to stall DNA replication and reduce gene expression via impairing the translation process in a repeat-length-dependent manner. Our results provide an unprecedented structural basis for understanding the pathogenic mechanism of AAGGG repeat expansion associated with CANVAS. In addition, the high-resolution structures resolved in this study will facilitate rational design of small-molecule ligands and helicases targeting G4s formed by AAGGG repeats for therapeutic interventions.
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Affiliation(s)
- Yang Wang
- School of Materials Science and Engineering, Tianjin University, Tianjin 300350, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Junyan Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Zhenzhen Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Jianing Hou
- Institute of Molecular Medicine (IMM) Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liqi Wan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yingquan Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Yu Liu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jie Yi
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Pei Guo
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Da Han
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Molecular Medicine (IMM) Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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21
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Xiong J, He Z, Wang L, Fan C, Chao J. DNA Origami-Enabled Gene Localization of Repetitive Sequences. J Am Chem Soc 2024; 146:6317-6325. [PMID: 38391280 DOI: 10.1021/jacs.4c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Repetitive sequences, which make up over 50% of human DNA, have diverse applications in disease diagnosis, forensic identification, paternity testing, and population genetic analysis due to their crucial functions for gene regulation. However, representative detection technologies such as sequencing and fluorescence imaging suffer from time-consuming protocols, high cost, and inaccuracy of the position and order of repetitive sequences. Here, we develop a precise and cost-effective strategy that combines the high resolution of atomic force microscopy with the shape customizability of DNA origami for repetitive sequence-specific gene localization. "Tri-block" DNA structures were specifically designed to connect repetitive sequences to DNA origami tags, thereby revealing precise genetic information in terms of position and sequence for high-resolution and high-precision visualization of repetitive sequences. More importantly, we achieved the results of simultaneous detection of different DNA repetitive sequences on the gene template with a resolution of ∼6.5 nm (19 nt). This strategy is characterized by high efficiency, high precision, low operational complexity, and low labor/time costs, providing a powerful complement to sequencing technologies for gene localization of repetitive sequences.
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Affiliation(s)
- Jinxin Xiong
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Zhimei He
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Lianhui Wang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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22
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Patiño-Guillén G, Pešović J, Panić M, Savić-Pavićević D, Bošković F, Keyser UF. Single-molecule RNA sizing enables quantitative analysis of alternative transcription termination. Nat Commun 2024; 15:1699. [PMID: 38402271 PMCID: PMC10894232 DOI: 10.1038/s41467-024-45968-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/01/2024] [Indexed: 02/26/2024] Open
Abstract
Transcription, a critical process in molecular biology, has found many applications in RNA synthesis, including mRNA vaccines and RNA therapeutics. However, current RNA characterization technologies suffer from amplification and enzymatic biases that lead to loss of native information. Here, we introduce a strategy to quantitatively study both transcription and RNA polymerase behaviour by sizing RNA with RNA nanotechnology and nanopores. To begin, we utilize T7 RNA polymerase to transcribe linear DNA lacking termination sequences. Surprisingly, we discover alternative transcription termination in the origin of replication sequence. Next, we employ circular DNA without transcription terminators to perform rolling circle transcription. This allows us to gain valuable insights into the processivity and transcription behaviour of RNA polymerase at the single-molecule level. Our work demonstrates how RNA nanotechnology and nanopores may be used in tandem for the direct and quantitative analysis of RNA transcripts. This methodology provides a promising pathway for accurate RNA structural mapping by enabling the study of full-length RNA transcripts at the single-molecule level.
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Affiliation(s)
| | - Jovan Pešović
- University of Belgrade - Faculty of Biology, Centre for Human Molecular Genetics, Belgrade, Serbia
| | - Marko Panić
- University of Belgrade - Faculty of Biology, Centre for Human Molecular Genetics, Belgrade, Serbia
- Institute of Virology, Vaccines and Sera "Torlak", Belgrade, Serbia
| | - Dušanka Savić-Pavićević
- University of Belgrade - Faculty of Biology, Centre for Human Molecular Genetics, Belgrade, Serbia
| | - Filip Bošković
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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23
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Arabfard M, Tajeddin N, Alizadeh S, Salesi M, Bayat H, Khorram Khorshid HR, Khamse S, Delbari A, Ohadi M. Dyads of GGC and GCC form hotspot colonies that coincide with the evolution of human and other great apes. BMC Genom Data 2024; 25:21. [PMID: 38383300 PMCID: PMC10880355 DOI: 10.1186/s12863-024-01207-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/11/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND GGC and GCC short tandem repeats (STRs) are of various evolutionary, biological, and pathological implications. However, the fundamental two-repeats (dyads) of these STRs are widely unexplored. RESULTS On a genome-wide scale, we mapped (GGC)2 and (GCC)2 dyads in human, and found monumental colonies (distance between each dyad < 500 bp) of extraordinary density, and in some instances periodicity. The largest (GCC)2 and (GGC)2 colonies were intergenic, homogeneous, and human-specific, consisting of 219 (GCC)2 on chromosome 2 (probability < 1.545E-219) and 70 (GGC)2 on chromosome 9 (probability = 1.809E-148). We also found that several colonies were shared in other great apes, and directionally increased in density and complexity in human, such as a colony of 99 (GCC)2 on chromosome 20, that specifically expanded in great apes, and reached maximum complexity in human (probability 1.545E-220). Numerous other colonies of evolutionary relevance in human were detected in other largely overlooked regions of the genome, such as chromosome Y and pseudogenes. Several of the genes containing or nearest to those colonies were divergently expressed in human. CONCLUSION In conclusion, (GCC)2 and (GGC)2 form unprecedented genomic colonies that coincide with the evolution of human and other great apes. The extent of the genomic rearrangements leading to those colonies support overlooked recombination hotspots, shared across great apes. The identified colonies deserve to be studied in mechanistic, evolutionary, and functional platforms.
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Affiliation(s)
- M Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Department of Biology, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Salesi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
- Research Center for Prevention of Oral and Dental Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - H Bayat
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H R Khorram Khorshid
- Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran
| | - S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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24
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Wan L, He A, Li J, Guo P, Han D. High-Resolution NMR Structures of Intrastrand Hairpins Formed by CTG Trinucleotide Repeats. ACS Chem Neurosci 2024; 15:868-876. [PMID: 38319692 DOI: 10.1021/acschemneuro.3c00769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
The CAG and CTG trinucleotide repeat expansions cause more than 10 human neurodegenerative diseases. Intrastrand hairpins formed by trinucleotide repeats contribute to repeat expansions, establishing them as potential drug targets. High-resolution structural determination of CAG and CTG hairpins poses as a long-standing goal to aid drug development, yet it has not been realized due to the intrinsic conformational flexibility of repetitive sequences. We herein investigate the solution structures of CTG hairpins using nuclear magnetic resonance (NMR) spectroscopy and found that four CTG repeats with a clamping G-C base pair was able to form a stable hairpin structure. We determine the first solution NMR structure of dG(CTG)4C hairpin and decipher a type I folding geometry of the TGCT tetraloop, wherein the two thymine residues form a T·T loop-closing base pair and the first three loop residues continuously stack. We further reveal that the CTG hairpin can be bound and stabilized by a small-molecule ligand, and the binding interferes with replication of a DNA template containing CTG repeats. Our determined high-resolution structures lay an important foundation for studying molecular interactions between native CTG hairpins and ligands, and benefit drug development for trinucleotide repeat expansion diseases.
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Affiliation(s)
- Liqi Wan
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Axin He
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jinxing Li
- ReviR Therapeutics, Shenzhen Bay Hi-Tech Ecological Park, Nanshan District, Shenzhen, Guangdong 518067, China
| | - Pei Guo
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Da Han
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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25
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Hannan AJ. Repeating themes of plastic genes and therapeutic schemes targeting the 'tandem repeatome'. Brain Commun 2024; 6:fcae047. [PMID: 38449715 PMCID: PMC10917440 DOI: 10.1093/braincomms/fcae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 01/24/2024] [Accepted: 02/17/2024] [Indexed: 03/08/2024] Open
Abstract
This scientific commentary refers to 'Modification of Huntington's disease by short tandem repeats' by Hong et al. (https://doi.org/10.1093/braincomms/fcae016) in Brain Communications.
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Affiliation(s)
- Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Australia
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Australia
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26
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Alizadeh S, Khamse S, Tajeddin N, Khorram Khorshid HR, Delbari A, Ohadi M. A GCC repeat in RAB26 undergoes natural selection in human and harbors divergent genotypes in late-onset Alzheimer's disease. Gene 2024; 893:147968. [PMID: 37931854 DOI: 10.1016/j.gene.2023.147968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
Although mainly located in genic regions and being mutation hotspots, intact blocks of CG-rich trinucleotide short tandem repeats (STRs) are largely overlooked with respect to their link with natural selection. The human RAB26 (member RAS oncogene family) directs synaptic and secretory vesicles into preautophagosomal structures, inhibition of which specifically disrupts axonal transport of degradative organelles and leads to an axonal dystrophy, resembling Alzheimer's disease (AD). Human RAB26 contains a GCC repeat in the top 1st percent in respect of length. Here we sequenced this STR in 441 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 216) and controls (N = 225). In both groups, the 12-repeat allele and the 12/12 genotype were predominantly abundant. We found excess of homozygosity for non-12 alleles in the NCD group (Mid-P exact = 0.027). Furthermore, divergent genotypes were detected that were specific to the NCD group (2.8% of genotypes) (Mid-P exact = 0.006) or controls (3.1% of genotypes) (Mid-P exact = 0.004). The patients harboring divergent genotypes received the diagnosis of AD. Based on the predominant abundance of the 12-repeat and 12/12 genotype in both groups, excess of non-12 homozygosity in the NCD group, and divergent genotypes across the NCD and control groups, we propose natural selection at this locus and link with late-onset AD. Our findings strengthen the hypothesis that a collection of rare genotypes unambiguously contribute to the pathogenesis of late-onset NCDs, such as AD.
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Affiliation(s)
- S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H R Khorram Khorshid
- Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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27
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Lu J, Toro C, Adams DR, Moreno CAM, Lee WP, Leung YY, Harms MB, Vardarajan B, Heinzen EL. LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants. BMC Genomics 2024; 25:115. [PMID: 38279154 PMCID: PMC10811831 DOI: 10.1186/s12864-023-09935-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 12/21/2023] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND Short tandem repeats (STRs) are widely distributed across the human genome and are associated with numerous neurological disorders. However, the extent that STRs contribute to disease is likely under-estimated because of the challenges calling these variants in short read next generation sequencing data. Several computational tools have been developed for STR variant calling, but none fully address all of the complexities associated with this variant class. RESULTS Here we introduce LUSTR which is designed to address some of the challenges associated with STR variant calling by enabling more flexibility in defining STR loci, allowing for customizable modules to tailor analyses, and expanding the capability to call somatic and multiallelic STR variants. LUSTR is a user-friendly and easily customizable tool for targeted or unbiased genome-wide STR variant screening that can use either predefined or novel genome builds. Using both simulated and real data sets, we demonstrated that LUSTR accurately infers germline and somatic STR expansions in individuals with and without diseases. CONCLUSIONS LUSTR offers a powerful and user-friendly approach that allows for the identification of STR variants and can facilitate more comprehensive studies evaluating the role of pathogenic STR variants across human diseases.
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Affiliation(s)
- Jinfeng Lu
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- The Taub Institute for Research On Alzheimer's Disease and the Aging Brain, Gertrude H. Sergievsky Center, Department of Neurology, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, NY, 10032, USA.
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, 20892, USA
| | - David R Adams
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Wan-Ping Lee
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory MedicinePerelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yuk Yee Leung
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory MedicinePerelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mathew B Harms
- Department of Neurology, Division of Neuromuscular Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Badri Vardarajan
- The Taub Institute for Research On Alzheimer's Disease and the Aging Brain, Gertrude H. Sergievsky Center, Department of Neurology, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York, NY, 10032, USA
| | - Erin L Heinzen
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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28
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Hong EP, Ramos EM, Aziz NA, Massey TH, McAllister B, Lobanov S, Jones L, Holmans P, Kwak S, Orth M, Ciosi M, Lomeikaite V, Monckton DG, Long JD, Lucente D, Wheeler VC, Gillis T, MacDonald ME, Sequeiros J, Gusella JF, Lee JM. Modification of Huntington's disease by short tandem repeats. Brain Commun 2024; 6:fcae016. [PMID: 38449714 PMCID: PMC10917446 DOI: 10.1093/braincomms/fcae016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/20/2023] [Accepted: 01/22/2024] [Indexed: 03/08/2024] Open
Abstract
Expansions of glutamine-coding CAG trinucleotide repeats cause a number of neurodegenerative diseases, including Huntington's disease and several of spinocerebellar ataxias. In general, age-at-onset of the polyglutamine diseases is inversely correlated with the size of the respective inherited expanded CAG repeat. Expanded CAG repeats are also somatically unstable in certain tissues, and age-at-onset of Huntington's disease corrected for individual HTT CAG repeat length (i.e. residual age-at-onset), is modified by repeat instability-related DNA maintenance/repair genes as demonstrated by recent genome-wide association studies. Modification of one polyglutamine disease (e.g. Huntington's disease) by the repeat length of another (e.g. ATXN3, CAG expansions in which cause spinocerebellar ataxia 3) has also been hypothesized. Consequently, we determined whether age-at-onset in Huntington's disease is modified by the CAG repeats of other polyglutamine disease genes. We found that the CAG measured repeat sizes of other polyglutamine disease genes that were polymorphic in Huntington's disease participants but did not influence Huntington's disease age-at-onset. Additional analysis focusing specifically on ATXN3 in a larger sample set (n = 1388) confirmed the lack of association between Huntington's disease residual age-at-onset and ATXN3 CAG repeat length. Additionally, neither our Huntington's disease onset modifier genome-wide association studies single nucleotide polymorphism data nor imputed short tandem repeat data supported the involvement of other polyglutamine disease genes in modifying Huntington's disease. By contrast, our genome-wide association studies based on imputed short tandem repeats revealed significant modification signals for other genomic regions. Together, our short tandem repeat genome-wide association studies show that modification of Huntington's disease is associated with short tandem repeats that do not involve other polyglutamine disease-causing genes, refining the landscape of Huntington's disease modification and highlighting the importance of rigorous data analysis, especially in genetic studies testing candidate modifiers.
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Affiliation(s)
- Eun Pyo Hong
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, The Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - Eliana Marisa Ramos
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - N Ahmad Aziz
- Population & Clinical Neuroepidemiology, German Center for Neurodegenerative Diseases, 53127 Bonn, Germany
- Department of Neurology, Faculty of Medicine, University of Bonn, Bonn D-53113, Germany
| | - Thomas H Massey
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Branduff McAllister
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Sergey Lobanov
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Lesley Jones
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Peter Holmans
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Seung Kwak
- Molecular System Biology, CHDI Foundation, Princeton, NJ 08540, USA
| | - Michael Orth
- University Hospital of Old Age Psychiatry and Psychotherapy, Bern University, CH-3000 Bern 60, Switzerland
| | - Marc Ciosi
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Vilija Lomeikaite
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Darren G Monckton
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Jeffrey D Long
- Department of Psychiatry, Carver College of Medicine and Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Diane Lucente
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vanessa C Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Tammy Gillis
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Marcy E MacDonald
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, The Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - Jorge Sequeiros
- UnIGENe, IBMC—Institute for Molecular and Cell Biology, i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto 420-135, Portugal
- ICBAS School of Medicine and Biomedical Sciences, University of Porto, Porto 420-135, Portugal
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics Program, The Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jong-Min Lee
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, The Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
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29
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Manigbas CA, Jadhav B, Garg P, Shadrina M, Lee W, Martin-Trujillo A, Sharp AJ. A phenome-wide association study of tandem repeat variation in 168,554 individuals from the UK Biobank. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.22.24301630. [PMID: 38343850 PMCID: PMC10854328 DOI: 10.1101/2024.01.22.24301630] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Most genetic association studies focus on binary variants. To identify the effects of multi-allelic variation of tandem repeats (TRs) on human traits, we performed direct TR genotyping and phenome-wide association studies in 168,554 individuals from the UK Biobank, identifying 47 TRs showing causal associations with 73 traits. We replicated 23 of 31 (74%) of these causal associations in the All of Us cohort. While this set included several known repeat expansion disorders, novel associations we found were attributable to common polymorphic variation in TR length rather than rare expansions and include e.g. a coding polyhistidine motif in HRCT1 influencing risk of hypertension and a poly(CGC) in the 5'UTR of GNB2 influencing heart rate. Causal TRs were strongly enriched for associations with local gene expression and DNA methylation. Our study highlights the contribution of multi-allelic TRs to the "missing heritability" of the human genome.
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30
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Jam HZ, Zook JM, Javadzadeh S, Park J, Sehgal A, Gymrek M. Genome-wide profiling of genetic variation at tandem repeat from long reads. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576266. [PMID: 38328152 PMCID: PMC10849534 DOI: 10.1101/2024.01.20.576266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve TR analysis, especially for long or complex repeats. Here we introduce LongTR, which accurately genotypes tandem repeats from high fidelity long reads available from both PacBio and Oxford Nanopore Technologies. LongTR is freely available at https://github.com/gymrek-lab/longtr.
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Affiliation(s)
- Helyaneh Ziaei Jam
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Justin M. Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD, USA
| | - Sara Javadzadeh
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Jonghun Park
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Aarushi Sehgal
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Melissa Gymrek
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
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31
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Zhang J, Zhu B. Short, but matters: short tandem repeats confer variation in transcription factor-DNA binding. Sci Bull (Beijing) 2024; 69:9-10. [PMID: 38042705 DOI: 10.1016/j.scib.2023.11.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2023]
Affiliation(s)
- Jing Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing 100101, China; New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing 100101, China; New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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32
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Dolzhenko E, English A, Dashnow H, De Sena Brandine G, Mokveld T, Rowell WJ, Karniski C, Kronenberg Z, Danzi MC, Cheung WA, Bi C, Farrow E, Wenger A, Chua KP, Martínez-Cerdeño V, Bartley TD, Jin P, Nelson DL, Zuchner S, Pastinen T, Quinlan AR, Sedlazeck FJ, Eberle MA. Characterization and visualization of tandem repeats at genome scale. Nat Biotechnol 2024:10.1038/s41587-023-02057-3. [PMID: 38168995 DOI: 10.1038/s41587-023-02057-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/06/2023] [Indexed: 01/05/2024]
Abstract
Tandem repeat (TR) variation is associated with gene expression changes and numerous rare monogenic diseases. Although long-read sequencing provides accurate full-length sequences and methylation of TRs, there is still a need for computational methods to profile TRs across the genome. Here we introduce the Tandem Repeat Genotyping Tool (TRGT) and an accompanying TR database. TRGT determines the consensus sequences and methylation levels of specified TRs from PacBio HiFi sequencing data. It also reports reads that support each repeat allele. These reads can be subsequently visualized with a companion TR visualization tool. Assessing 937,122 TRs, TRGT showed a Mendelian concordance of 98.38%, allowing a single repeat unit difference. In six samples with known repeat expansions, TRGT detected all expansions while also identifying methylation signals and mosaicism and providing finer repeat length resolution than existing methods. Additionally, we released a database with allele sequences and methylation levels for 937,122 TRs across 100 genomes.
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Affiliation(s)
| | - Adam English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Harriet Dashnow
- Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
| | | | - Tom Mokveld
- Pacific Biosciences of California, Menlo Park, CA, USA
| | | | | | | | - Matt C Danzi
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Chengpeng Bi
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Emily Farrow
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Aaron Wenger
- Pacific Biosciences of California, Menlo Park, CA, USA
| | - Khi Pin Chua
- Pacific Biosciences of California, Menlo Park, CA, USA
| | - Verónica Martínez-Cerdeño
- Institute for Pediatric Regenerative Medicine, Shriner's Hospital for Children and UC Davis School of Medicine, Sacramento, CA, USA
- Department of Pathology & Laboratory Medicine, UC Davis School of Medicine, Sacramento, CA, USA
- MIND Institute, UC Davis School of Medicine, Sacramento, CA, USA
| | - Trevor D Bartley
- Institute for Pediatric Regenerative Medicine, Shriner's Hospital for Children and UC Davis School of Medicine, Sacramento, CA, USA
- Department of Pathology & Laboratory Medicine, UC Davis School of Medicine, Sacramento, CA, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - David L Nelson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Aaron R Quinlan
- Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
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33
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Ito H, Machida K, Hasumi M, Ueyama M, Nagai Y, Imataka H, Taguchi H. Reconstitution of C9orf72 GGGGCC repeat-associated non-AUG translation with purified human translation factors. Sci Rep 2023; 13:22826. [PMID: 38129650 PMCID: PMC10739749 DOI: 10.1038/s41598-023-50188-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023] Open
Abstract
Nucleotide repeat expansion of GGGGCC (G4C2) in the non-coding region of C9orf72 is the most common genetic cause underlying amyotrophic lateral sclerosis and frontotemporal dementia. Transcripts harboring this repeat expansion undergo the translation of dipeptide repeats via a non-canonical process known as repeat-associated non-AUG (RAN) translation. In order to ascertain the essential components required for RAN translation, we successfully recapitulated G4C2-RAN translation using an in vitro reconstituted translation system comprising human factors, namely the human PURE system. Our findings conclusively demonstrate that the presence of fundamental translation factors is sufficient to mediate the elongation from the G4C2 repeat. Furthermore, the initiation mechanism proceeded in a 5' cap-dependent manner, independent of eIF2A or eIF2D. In contrast to cell lysate-mediated RAN translation, where longer G4C2 repeats enhanced translation, we discovered that the expansion of the G4C2 repeats inhibited translation elongation using the human PURE system. These results suggest that the repeat RNA itself functions as a repressor of RAN translation. Taken together, our utilization of a reconstituted RAN translation system employing minimal factors represents a distinctive and potent approach for elucidating the intricacies underlying RAN translation mechanism.
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Grants
- JPMJFS2112 Japan Science and Technology Agency
- JP26116002 Ministry of Education, Culture, Sports, Science and Technology
- JP18H03984 Ministry of Education, Culture, Sports, Science and Technology
- JP21H04763 Ministry of Education, Culture, Sports, Science and Technology
- JP20H05925 Ministry of Education, Culture, Sports, Science and Technology
- 2019-25 Mitsubishi Foundation
- 2019 Uehara Memorial Foundation
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Affiliation(s)
- Hayato Ito
- School of Life Science and Technology, Tokyo Institute of Technology, S2-19, Nagatsuta 4259, Midori-ku, Yokohama, 226-8501, Japan
| | - Kodai Machida
- Graduate School of Engineering, University of Hyogo, Shosha, 2167, Himeji, Hyogo, 671-2280, Japan
| | - Mayuka Hasumi
- School of Life Science and Technology, Tokyo Institute of Technology, S2-19, Nagatsuta 4259, Midori-ku, Yokohama, 226-8501, Japan
| | - Morio Ueyama
- Department of Neurology, Faculty of Medicine, Kindai University, Ohonohigashi 377-2, Osaka-Sayama, 589-8511, Japan
| | - Yoshitaka Nagai
- Department of Neurology, Faculty of Medicine, Kindai University, Ohonohigashi 377-2, Osaka-Sayama, 589-8511, Japan
| | - Hiroaki Imataka
- Graduate School of Engineering, University of Hyogo, Shosha, 2167, Himeji, Hyogo, 671-2280, Japan
| | - Hideki Taguchi
- School of Life Science and Technology, Tokyo Institute of Technology, S2-19, Nagatsuta 4259, Midori-ku, Yokohama, 226-8501, Japan.
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, S2-19, Nagatsuta 4259, Midori-ku, Yokohama, 226-8501, Japan.
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34
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Rajagopal S, Donaldson J, Flower M, Hensman Moss DJ, Tabrizi SJ. Genetic modifiers of repeat expansion disorders. Emerg Top Life Sci 2023; 7:325-337. [PMID: 37861103 PMCID: PMC10754329 DOI: 10.1042/etls20230015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/20/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023]
Abstract
Repeat expansion disorders (REDs) are monogenic diseases caused by a sequence of repetitive DNA expanding above a pathogenic threshold. A common feature of the REDs is a strong genotype-phenotype correlation in which a major determinant of age at onset (AAO) and disease progression is the length of the inherited repeat tract. Over a disease-gene carrier's life, the length of the repeat can expand in somatic cells, through the process of somatic expansion which is hypothesised to drive disease progression. Despite being monogenic, individual REDs are phenotypically variable, and exploring what genetic modifying factors drive this phenotypic variability has illuminated key pathogenic mechanisms that are common to this group of diseases. Disease phenotypes are affected by the cognate gene in which the expansion is found, the location of the repeat sequence in coding or non-coding regions and by the presence of repeat sequence interruptions. Human genetic data, mouse models and in vitro models have implicated the disease-modifying effect of DNA repair pathways via the mechanisms of somatic mutation of the repeat tract. As such, developing an understanding of these pathways in the context of expanded repeats could lead to future disease-modifying therapies for REDs.
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Affiliation(s)
- Sangeerthana Rajagopal
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
| | - Jasmine Donaldson
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
| | - Michael Flower
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
| | - Davina J Hensman Moss
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
- St George's University of London, London SW17 0RE, U.K
| | - Sarah J Tabrizi
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, U.K
- UK Dementia Research Institute, University College London, London WCC1N 3BG, U.K
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35
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Panoyan MA, Wendt FR. The role of tandem repeat expansions in brain disorders. Emerg Top Life Sci 2023; 7:249-263. [PMID: 37401564 DOI: 10.1042/etls20230022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/05/2023] [Accepted: 06/19/2023] [Indexed: 07/05/2023]
Abstract
The human genome contains numerous genetic polymorphisms contributing to different health and disease outcomes. Tandem repeat (TR) loci are highly polymorphic yet under-investigated in large genomic studies, which has prompted research efforts to identify novel variations and gain a deeper understanding of their role in human biology and disease outcomes. We summarize the current understanding of TRs and their implications for human health and disease, including an overview of the challenges encountered when conducting TR analyses and potential solutions to overcome these challenges. By shedding light on these issues, this article aims to contribute to a better understanding of the impact of TRs on the development of new disease treatments.
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Affiliation(s)
- Mary Anne Panoyan
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
| | - Frank R Wendt
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Forensic Science Program, University of Toronto, Mississauga, ON, Canada
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Read JL, Davies KC, Thompson GC, Delatycki MB, Lockhart PJ. Challenges facing repeat expansion identification, characterisation, and the pathway to discovery. Emerg Top Life Sci 2023; 7:339-348. [PMID: 37888797 PMCID: PMC10754332 DOI: 10.1042/etls20230019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023]
Abstract
Tandem repeat DNA sequences constitute a significant proportion of the human genome. While previously considered to be functionally inert, these sequences are now broadly accepted as important contributors to genetic diversity. However, the polymorphic nature of these sequences can lead to expansion beyond a gene-specific threshold, causing disease. More than 50 pathogenic repeat expansions have been identified to date, many of which have been discovered in the last decade as a result of advances in sequencing technologies and associated bioinformatic tools. Commonly utilised diagnostic platforms including Sanger sequencing, capillary array electrophoresis, and Southern blot are generally low throughput and are often unable to accurately determine repeat size, composition, and epigenetic signature, which are important when characterising repeat expansions. The rapid advances in bioinformatic tools designed specifically to interrogate short-read sequencing and the development of long-read single molecule sequencing is enabling a new generation of high throughput testing for repeat expansion disorders. In this review, we discuss some of the challenges surrounding the identification and characterisation of disease-causing repeat expansions and the technological advances that are poised to translate the promise of genomic medicine to individuals and families affected by these disorders.
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Affiliation(s)
- Justin L Read
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Kayli C Davies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Genevieve C Thompson
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Parkville, Victoria, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
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Loh PR. Uncovering complex trait heritability hidden in the repeatome. CELL GENOMICS 2023; 3:100461. [PMID: 38116125 PMCID: PMC10726486 DOI: 10.1016/j.xgen.2023.100461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Short tandem repeats (STRs) account for a substantial fraction of human genetic variation, but their contribution to complex human phenotypes is largely unknown. Margoliash et al. perform detailed genome-wide association analysis and fine-mapping of STRs in UK Biobank, identifying many STRs likely to influence variation in blood and serum traits.
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Affiliation(s)
- Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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38
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Hannan AJ. Expanding horizons of tandem repeats in biology and medicine: Why 'genomic dark matter' matters. Emerg Top Life Sci 2023; 7:ETLS20230075. [PMID: 38088823 PMCID: PMC10754335 DOI: 10.1042/etls20230075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023]
Abstract
Approximately half of the human genome includes repetitive sequences, and these DNA sequences (as well as their transcribed repetitive RNA and translated amino-acid repeat sequences) are known as the repeatome. Within this repeatome there are a couple of million tandem repeats, dispersed throughout the genome. These tandem repeats have been estimated to constitute ∼8% of the entire human genome. These tandem repeats can be located throughout exons, introns and intergenic regions, thus potentially affecting the structure and function of tandemly repetitive DNA, RNA and protein sequences. Over more than three decades, more than 60 monogenic human disorders have been found to be caused by tandem-repeat mutations. These monogenic tandem-repeat disorders include Huntington's disease, a variety of ataxias, amyotrophic lateral sclerosis and frontotemporal dementia, as well as many other neurodegenerative diseases. Furthermore, tandem-repeat disorders can include fragile X syndrome, related fragile X disorders, as well as other neurological and psychiatric disorders. However, these monogenic tandem-repeat disorders, which were discovered via their dominant or recessive modes of inheritance, may represent the 'tip of the iceberg' with respect to tandem-repeat contributions to human disorders. A previous proposal that tandem repeats may contribute to the 'missing heritability' of various common polygenic human disorders has recently been supported by a variety of new evidence. This includes genome-wide studies that associate tandem-repeat mutations with autism, schizophrenia, Parkinson's disease and various types of cancers. In this article, I will discuss how tandem-repeat mutations and polymorphisms could contribute to a wide range of common disorders, along with some of the many major challenges of tandem-repeat biology and medicine. Finally, I will discuss the potential of tandem repeats to be therapeutically targeted, so as to prevent and treat an expanding range of human disorders.
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Affiliation(s)
- Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Anatomy and Physiology, University of Melbourne, Parkville, Victoria 3010, Australia
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Gao J, Sun W, Li J, Ban H, Zhang T, Liao J, Kim N, Lee SH, Dong Q, Madramootoo R, Chen Y, Li F. Rex1BD and the 14-3-3 protein control heterochromatin organization at tandem repeats by linking RNAi and HDAC. Proc Natl Acad Sci U S A 2023; 120:e2309359120. [PMID: 38048463 PMCID: PMC10723143 DOI: 10.1073/pnas.2309359120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/30/2023] [Indexed: 12/06/2023] Open
Abstract
Tandem DNA repeats are often organized into heterochromatin that is crucial for genome organization and stability. Recent studies revealed that individual repeats within tandem DNA repeats can behave very differently. How DNA repeats are assembled into distinct heterochromatin structures remains poorly understood. Here, we developed a genome-wide genetic screen using a reporter gene at different units in a repeat array. This screen led to identification of a conserved protein Rex1BD required for heterochromatin silencing. Our structural analysis revealed that Rex1BD forms a four-helix bundle structure with a distinct charged electrostatic surface. Mechanistically, Rex1BD facilitates the recruitment of Clr6 histone deacetylase (HDAC) by interacting with histones. Interestingly, Rex1BD also interacts with the 14-3-3 protein Rad25, which is responsible for recruiting the RITS (RNA-induced transcriptional silencing) complex to DNA repeats. Our results suggest that coordinated action of Rex1BD and Rad25 mediates formation of distinct heterochromatin structure at DNA repeats via linking RNAi and HDAC pathways.
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Affiliation(s)
- Jinxin Gao
- Department of Biology, New York University, New York, NY10003
| | - Wenqi Sun
- Key Laboratory of Epigenetic Regulation and Intervention, State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Jie Li
- National Facility for Protein Science Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai201210, China
| | - Hyoju Ban
- Department of Biology, New York University, New York, NY10003
| | - Tuokai Zhang
- Department of Biology, New York University, New York, NY10003
| | - Junwei Liao
- Department of Biology, New York University, New York, NY10003
| | - Namho Kim
- Department of Biology, New York University, New York, NY10003
| | - Soon Hoo Lee
- Department of Biology, New York University, New York, NY10003
| | - Qianhua Dong
- Department of Biology, New York University, New York, NY10003
| | | | - Yong Chen
- Key Laboratory of Epigenetic Regulation and Intervention, State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
| | - Fei Li
- Department of Biology, New York University, New York, NY10003
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Felício D, du Mérac TR, Amorim A, Martins S. Functional implications of paralog genes in polyglutamine spinocerebellar ataxias. Hum Genet 2023; 142:1651-1676. [PMID: 37845370 PMCID: PMC10676324 DOI: 10.1007/s00439-023-02607-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/22/2023] [Indexed: 10/18/2023]
Abstract
Polyglutamine (polyQ) spinocerebellar ataxias (SCAs) comprise a group of autosomal dominant neurodegenerative disorders caused by (CAG/CAA)n expansions. The elongated stretches of adjacent glutamines alter the conformation of the native proteins inducing neurotoxicity, and subsequent motor and neurological symptoms. Although the etiology and neuropathology of most polyQ SCAs have been extensively studied, only a limited selection of therapies is available. Previous studies on SCA1 demonstrated that ATXN1L, a human duplicated gene of the disease-associated ATXN1, alleviated neuropathology in mice models. Other SCA-associated genes have paralogs (i.e., copies at different chromosomal locations derived from duplication of the parental gene), but their functional relevance and potential role in disease pathogenesis remain unexplored. Here, we review the protein homology, expression pattern, and molecular functions of paralogs in seven polyQ dominant ataxias-SCA1, SCA2, MJD/SCA3, SCA6, SCA7, SCA17, and DRPLA. Besides ATXN1L, we highlight ATXN2L, ATXN3L, CACNA1B, ATXN7L1, ATXN7L2, TBPL2, and RERE as promising functional candidates to play a role in the neuropathology of the respective SCA, along with the parental gene. Although most of these duplicates lack the (CAG/CAA)n region, if functionally redundant, they may compensate for a partial loss-of-function or dysfunction of the wild-type genes in SCAs. We aim to draw attention to the hypothesis that paralogs of disease-associated genes may underlie the complex neuropathology of dominant ataxias and potentiate new therapeutic strategies.
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Affiliation(s)
- Daniela Felício
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313, Porto, Portugal
| | - Tanguy Rubat du Mérac
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Faculty of Science, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal
| | - Sandra Martins
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135, Porto, Portugal.
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135, Porto, Portugal.
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Wang Z, Castillo-González CM, Zhao C, Tong CY, Li C, Zhong S, Liu Z, Xie K, Zhu J, Wu Z, Peng X, Jacob Y, Michaels SD, Jacobsen SE, Zhang X. H3.1K27me1 loss confers Arabidopsis resistance to Geminivirus by sequestering DNA repair proteins onto host genome. Nat Commun 2023; 14:7484. [PMID: 37980416 PMCID: PMC10657422 DOI: 10.1038/s41467-023-43311-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/06/2023] [Indexed: 11/20/2023] Open
Abstract
The H3 methyltransferases ATXR5 and ATXR6 deposit H3.1K27me1 to heterochromatin to prevent genomic instability and transposon re-activation. Here, we report that atxr5 atxr6 mutants display robust resistance to Geminivirus. The viral resistance is correlated with activation of DNA repair pathways, but not with transposon re-activation or heterochromatin amplification. We identify RAD51 and RPA1A as partners of virus-encoded Rep protein. The two DNA repair proteins show increased binding to heterochromatic regions and defense-related genes in atxr5 atxr6 vs wild-type plants. Consequently, the proteins have reduced binding to viral DNA in the mutant, thus hampering viral amplification. Additionally, RAD51 recruitment to the host genome arise via BRCA1, HOP2, and CYCB1;1, and this recruitment is essential for viral resistance in atxr5 atxr6. Thus, Geminiviruses adapt to healthy plants by hijacking DNA repair pathways, whereas the unstable genome, triggered by reduced H3.1K27me1, could retain DNA repairing proteins to suppress viral amplification in atxr5 atxr6.
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Affiliation(s)
- Zhen Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
- Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX, 77843, USA
| | | | - Changjiang Zhao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Chun-Yip Tong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Changhao Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Songxiao Zhong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Zhiyang Liu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Kaili Xie
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Jiaying Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Zhongshou Wu
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Xu Peng
- Department of Molecular Physiology, College of Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Yannick Jacob
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Scott D Michaels
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
- Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX, 77843, USA.
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
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42
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Guo MH, Lee WP, Vardarajan B, Schellenberg GD, Phillips-Cremins J. Polygenic burden of short tandem repeat expansions promote risk for Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.16.23298623. [PMID: 38014121 PMCID: PMC10680900 DOI: 10.1101/2023.11.16.23298623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Studies of the genetics of Alzheimer's disease (AD) have largely focused on single nucleotide variants and short insertions/deletions. However, most of the disease heritability has yet to be uncovered, suggesting that there is substantial genetic risk conferred by other forms of genetic variation. There are over one million short tandem repeats (STRs) in the genome, and their link to AD risk has not been assessed. As pathogenic expansions of STR cause over 30 neurologic diseases, it is important to ascertain whether STRs may also be implicated in AD risk. Here, we genotyped 321,742 polymorphic STR tracts genome-wide using PCR-free whole genome sequencing data from 2,981 individuals (1,489 AD case and 1,492 control individuals). We implemented an approach to identify STR expansions as STRs with tract lengths that are outliers from the population. We then tested for differences in aggregate burden of expansions in case versus control individuals. AD patients had a 1.19-fold increase of STR expansions compared to healthy elderly controls (p=8.27×10-3, two-sided Mann Whitney test). Individuals carrying > 30 STR expansions had 3.62-fold higher odds of having AD and had more severe AD neuropathology. AD STR expansions were highly enriched within active promoters in post-mortem hippocampal brain tissues and particularly within SINE-VNTR-Alu (SVA) retrotransposons. Together, these results demonstrate that expanded STRs within active promoter regions of the genome promote risk of AD.
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Affiliation(s)
- Michael H Guo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Badri Vardarajan
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jennifer Phillips-Cremins
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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43
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English A, Dolzhenko E, Jam HZ, Mckenzie S, Olson ND, De Coster W, Park J, Gu B, Wagner J, Eberle MA, Gymrek M, Chaisson MJP, Zook JM, Sedlazeck FJ. Benchmarking of small and large variants across tandem repeats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.29.564632. [PMID: 37961319 PMCID: PMC10634962 DOI: 10.1101/2023.10.29.564632] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Tandem repeats (TRs) are highly polymorphic in the human genome, have thousands of associated molecular traits, and are linked to over 60 disease phenotypes. However, their complexity often excludes them from at-scale studies due to challenges with variant calling, representation, and lack of a genome-wide standard. To promote TR methods development, we create a comprehensive catalog of TR regions and explore its properties across 86 samples. We then curate variants from the GIAB HG002 individual to create a tandem repeat benchmark. We also present a variant comparison method that handles small and large alleles and varying allelic representation. The 8.1% of the genome covered by the TR catalog holds ∼24.9% of variants per individual, including 124,728 small and 17,988 large variants for the GIAB HG002 TR benchmark. We work with the GIAB community to demonstrate the utility of this benchmark across short and long read technologies.
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Gambelli A, Ferrando A, Boncristiani C, Schoeftner S. Regulation and function of R-loops at repetitive elements. Biochimie 2023; 214:141-155. [PMID: 37619810 DOI: 10.1016/j.biochi.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/13/2023] [Accepted: 08/19/2023] [Indexed: 08/26/2023]
Abstract
R-loops are atypical, three-stranded nucleic acid structures that contain a stretch of RNA:DNA hybrids and an unpaired, single stranded DNA loop. R-loops are physiological relevant and can act as regulators of gene expression, chromatin structure, DNA damage repair and DNA replication. However, unscheduled and persistent R-loops are mutagenic and can mediate replication-transcription conflicts, leading to DNA damage and genome instability if left unchecked. Detailed transcriptome analysis unveiled that 85% of the human genome, including repetitive regions, hold transcriptional activity. This anticipates that R-loops management plays a central role for the regulation and integrity of genomes. This function is expected to have a particular relevance for repetitive sequences that make up to 75% of the human genome. Here, we review the impact of R-loops on the function and stability of repetitive regions such as centromeres, telomeres, rDNA arrays, transposable elements and triplet repeat expansions and discuss their relevance for associated pathological conditions.
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Affiliation(s)
- Alice Gambelli
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Alessandro Ferrando
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Chiara Boncristiani
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Stefan Schoeftner
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy.
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45
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Doyle LA, Takushi B, Kibler RD, Milles LF, Orozco CT, Jones JD, Jackson SE, Stoddard BL, Bradley P. De novo design of knotted tandem repeat proteins. Nat Commun 2023; 14:6746. [PMID: 37875492 PMCID: PMC10598012 DOI: 10.1038/s41467-023-42388-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
De novo protein design methods can create proteins with folds not yet seen in nature. These methods largely focus on optimizing the compatibility between the designed sequence and the intended conformation, without explicit consideration of protein folding pathways. Deeply knotted proteins, whose topologies may introduce substantial barriers to folding, thus represent an interesting test case for protein design. Here we report our attempts to design proteins with trefoil (31) and pentafoil (51) knotted topologies. We extended previously described algorithms for tandem repeat protein design in order to construct deeply knotted backbones and matching designed repeat sequences (N = 3 repeats for the trefoil and N = 5 for the pentafoil). We confirmed the intended conformation for the trefoil design by X ray crystallography, and we report here on this protein's structure, stability, and folding behaviour. The pentafoil design misfolded into an asymmetric structure (despite a 5-fold symmetric sequence); two of the four repeat-repeat units matched the designed backbone while the other two diverged to form local contacts, leading to a trefoil rather than pentafoil knotted topology. Our results also provide insights into the folding of knotted proteins.
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Affiliation(s)
- Lindsey A Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Brittany Takushi
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Ryan D Kibler
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Lukas F Milles
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Carolina T Orozco
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Jonathan D Jones
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sophie E Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA.
| | - Philip Bradley
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA.
- Division of Public Health Sciences and Program in Computational Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N, Seattle, WA, 98009, USA.
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46
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Ziaei Jam H, Li Y, DeVito R, Mousavi N, Ma N, Lujumba I, Adam Y, Maksimov M, Huang B, Dolzhenko E, Qiu Y, Kakembo FE, Joseph H, Onyido B, Adeyemi J, Bakhtiari M, Park J, Javadzadeh S, Jjingo D, Adebiyi E, Bafna V, Gymrek M. A deep population reference panel of tandem repeat variation. Nat Commun 2023; 14:6711. [PMID: 37872149 PMCID: PMC10593948 DOI: 10.1038/s41467-023-42278-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 10/05/2023] [Indexed: 10/25/2023] Open
Abstract
Tandem repeats (TRs) represent one of the largest sources of genetic variation in humans and are implicated in a range of phenotypes. Here we present a deep characterization of TR variation based on high coverage whole genome sequencing from 3550 diverse individuals from the 1000 Genomes Project and H3Africa cohorts. We develop a method, EnsembleTR, to integrate genotypes from four separate methods resulting in high-quality genotypes at more than 1.7 million TR loci. Our catalog reveals novel sequence features influencing TR heterozygosity, identifies population-specific trinucleotide expansions, and finds hundreds of novel eQTL signals. Finally, we generate a phased haplotype panel which can be used to impute most TRs from nearby single nucleotide polymorphisms (SNPs) with high accuracy. Overall, the TR genotypes and reference haplotype panel generated here will serve as valuable resources for future genome-wide and population-wide studies of TRs and their role in human phenotypes.
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Affiliation(s)
- Helyaneh Ziaei Jam
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Yang Li
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ross DeVito
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Nima Mousavi
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Nichole Ma
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ibra Lujumba
- The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Yagoub Adam
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun, 112233, Nigeria
| | - Mikhail Maksimov
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Bonnie Huang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | - Yunjiang Qiu
- Illumina Incorporated, San Diego, CA, 92122, USA
| | - Fredrick Elishama Kakembo
- The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Habi Joseph
- The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Blessing Onyido
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun, 112233, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun, 112233, Nigeria
| | - Jumoke Adeyemi
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun, 112233, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun, 112233, Nigeria
| | - Mehrdad Bakhtiari
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Jonghun Park
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Sara Javadzadeh
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Daudi Jjingo
- The African Center of Excellence in Bioinformatics and Data Intensive Sciences, the Infectious Diseases Institute, Makerere University, Kampala, Uganda
- Department of Computer Science, Makerere University, Kampala, Uganda
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun, 112233, Nigeria
- Department of Computer & Information Sciences, Covenant University, Ota, Ogun, 112233, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota, Ogun, 112233, Nigeria
- Applied Bioinformatics Division, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, 69120, Germany
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Melissa Gymrek
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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47
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Sathyaseelan C, Veerapathiran S, Das U, Ravichandran G, Ajjugal Y, Singh J, Rengan AK, Rathinavelan T, Prabusankar G. Destabilizing Effect of Organo Ru(II) Salts on the Intermolecular Parallel CGG Repeat DNA Quadruplex Associated with Neurodegenerative/Neuromuscular Diseases. ACS Chem Neurosci 2023; 14:3646-3654. [PMID: 37698929 DOI: 10.1021/acschemneuro.3c00285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023] Open
Abstract
The cationic organo ruthenium(II) salts ([Ru(p-cymene)(ipit)(Cl)](Cl) (RuS), 1-isopropyl-3-(pyridin-2-yl)-imidazol-2-thione (ipit) and [Ru(p-cymene)(ipis)(Cl)](Cl) (RuSe), 1-isopropyl-3-(pyridin-2-yl)-imidazol-2-selenone (ipis)) are isolated, and their binding efficacy with d(CGG)15 quadruplex is investigated. Circular dichroism (CD) wavelength scan titration experiments of RuS and RuSe compounds with the intermolecular parallel quadruplex formed by d(CGG)15 (associated with neurodegenerative/neuromuscular/neuronal intranuclear inclusion disorders like FXTAS, OPMD, OPDM types 1-4, and OPML as well as FXPOI) and with the control d(CGG)15·d(CCG)15 duplex indicate their specificity toward the former. Electrophoretic mobility shift titration experiments also confirm the binding of the ligands with d(CGG)15. CD thermal denaturation experiments indicate that both RuS and RuSe destabilize the quadruplex, specifically at 10 mM concentration of the ligands. This is further confirmed by 1D 1H NMR experiments. Such a destabilizing effect of these ligands on the d(CGG)15 quadruplex indicates that RuS and RuSe chalcogen complexes can act as a template for the design of novel molecules for the diagnostics and/or therapeutics of CGG repeat expansion-associated diseases.
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Affiliation(s)
- Chakkarai Sathyaseelan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Hyderabad 502284, India
| | - Sabari Veerapathiran
- Organometallics and Materials Chemistry Lab, Department of Chemistry, Indian Institute of Technology Hyderabad, Hyderabad 502284, India
| | - Uttam Das
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Hyderabad 502284, India
| | - Gayathri Ravichandran
- Biomedical Engineering, Indian Institute of Technology Hyderabad, Hyderabad 502284, India
| | - Yogeeshwar Ajjugal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Hyderabad 502284, India
| | - Joginder Singh
- Organometallics and Materials Chemistry Lab, Department of Chemistry, Indian Institute of Technology Hyderabad, Hyderabad 502284, India
| | - Aravind Kumar Rengan
- Biomedical Engineering, Indian Institute of Technology Hyderabad, Hyderabad 502284, India
| | | | - Ganesan Prabusankar
- Organometallics and Materials Chemistry Lab, Department of Chemistry, Indian Institute of Technology Hyderabad, Hyderabad 502284, India
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48
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Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Suzuki PH, Shrikumar A, Afek A, Greenleaf WJ, Gordân R, Zeitlinger J, Kundaje A, Fordyce PM. Short tandem repeats bind transcription factors to tune eukaryotic gene expression. Science 2023; 381:eadd1250. [PMID: 37733848 DOI: 10.1126/science.add1250] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/26/2023] [Indexed: 09/23/2023]
Abstract
Short tandem repeats (STRs) are enriched in eukaryotic cis-regulatory elements and alter gene expression, yet how they regulate transcription remains unknown. We found that STRs modulate transcription factor (TF)-DNA affinities and apparent on-rates by about 70-fold by directly binding TF DNA-binding domains, with energetic impacts exceeding many consensus motif mutations. STRs maximize the number of weakly preferred microstates near target sites, thereby increasing TF density, with impacts well predicted by statistical mechanics. Confirming that STRs also affect TF binding in cells, neural networks trained only on in vivo occupancies predicted effects identical to those observed in vitro. Approximately 90% of TFs preferentially bound STRs that need not resemble known motifs, providing a cis-regulatory mechanism to target TFs to genomic sites.
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Affiliation(s)
- Connor A Horton
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Amr M Alexandari
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Michael G B Hayes
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Emil Marklund
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julia M Schaepe
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Arjun K Aditham
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Nilay Shah
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Peter H Suzuki
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Avanti Shrikumar
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Ariel Afek
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Computer Science, Duke University, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- The University of Kansas Medical Center, Kansas City, KS 66103, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Polly M Fordyce
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94110, USA
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49
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Liao X, Zhu W, Zhou J, Li H, Xu X, Zhang B, Gao X. Repetitive DNA sequence detection and its role in the human genome. Commun Biol 2023; 6:954. [PMID: 37726397 PMCID: PMC10509279 DOI: 10.1038/s42003-023-05322-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/04/2023] [Indexed: 09/21/2023] Open
Abstract
Repetitive DNA sequences playing critical roles in driving evolution, inducing variation, and regulating gene expression. In this review, we summarized the definition, arrangement, and structural characteristics of repeats. Besides, we introduced diverse biological functions of repeats and reviewed existing methods for automatic repeat detection, classification, and masking. Finally, we analyzed the type, structure, and regulation of repeats in the human genome and their role in the induction of complex diseases. We believe that this review will facilitate a comprehensive understanding of repeats and provide guidance for repeat annotation and in-depth exploration of its association with human diseases.
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Affiliation(s)
- Xingyu Liao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Wufei Zhu
- Department of Endocrinology, Yichang Central People's Hospital, The First College of Clinical Medical Science, China Three Gorges University, 443000, Yichang, P.R. China
| | - Juexiao Zhou
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Haoyang Li
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Xiaopeng Xu
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Bin Zhang
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia.
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50
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Vasunilashorn SM, Dillon ST, Marcantonio ER, Libermann TA. Application of Multiple Omics to Understand Postoperative Delirium Pathophysiology in Humans. Gerontology 2023; 69:1369-1384. [PMID: 37722373 PMCID: PMC10711777 DOI: 10.1159/000533789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023] Open
Abstract
Delirium, an acute change in cognition, is common, morbid, and costly, particularly among hospitalized older adults. Despite growing knowledge of its epidemiology, far less is known about delirium pathophysiology. Initial work understanding delirium pathogenesis has focused on assaying single or a limited subset of molecules or genetic loci. Recent technological advances at the forefront of biomarker and drug target discovery have facilitated application of multiple "omics" approaches aimed to provide a more complete understanding of complex disease processes such as delirium. At its basic level, "omics" involves comparison of genes (genomics, epigenomics), transcripts (transcriptomics), proteins (proteomics), metabolites (metabolomics), or lipids (lipidomics) in biological fluids or tissues obtained from patients who have a certain condition (i.e., delirium) and those who do not. Multi-omics analyses of these various types of molecules combined with machine learning and systems biology enable the discovery of biomarkers, biological pathways, and predictors of delirium, thus elucidating its pathophysiology. This review provides an overview of the most recent omics techniques, their current impact on identifying delirium biomarkers, and future potential in enhancing our understanding of delirium pathogenesis. We summarize challenges in identification of specific biomarkers of delirium and, more importantly, in discovering the mechanisms underlying delirium pathophysiology. Based on mounting evidence, we highlight a heightened inflammatory response as one common pathway in delirium risk and progression, and we suggest other promising biological mechanisms that have recently emerged. Advanced multiple omics approaches coupled with bioinformatics methodologies have great promise to yield important discoveries that will advance delirium research.
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Affiliation(s)
- Sarinnapha M. Vasunilashorn
- Division of General Medicine, Department of Medicine, Beth Israel Deaconess Medical Center (BIDMC), Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Simon T. Dillon
- Harvard Medical School, Boston, MA, USA
- Division of Interdisciplinary Medicine and Biotechnology, Department of Medicine, BIDMC, Boston, MA, USA
- Genomics, Proteomics, Bioinformatics and Systems Biology Center, BIDMC, Boston, MA, USA
| | - Edward R. Marcantonio
- Division of General Medicine, Department of Medicine, Beth Israel Deaconess Medical Center (BIDMC), Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gerontology, Department of Medicine, BIDMC, Boston, MA, USA
| | - Towia A. Libermann
- Harvard Medical School, Boston, MA, USA
- Division of Interdisciplinary Medicine and Biotechnology, Department of Medicine, BIDMC, Boston, MA, USA
- Genomics, Proteomics, Bioinformatics and Systems Biology Center, BIDMC, Boston, MA, USA
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